The blame game on why there are so few fish around in the Strait of Georgia is always an interesting one. FN, Commies, Rec, fishfarms, seals, pathogens, habitat degradation, climate change, etc all part no doubt. We can and do spend countless hours blaming each other but for these woeful returns but research in the strait (and cowichan in particular) is showing that the BIG issue is not FN, Commie or Rec fisheries that are taking/harvesting these returning fish. The BIG issues is juvenile mortality. How big? The research teams working on this with tagged juvenile salmon believe it could be around 60-80% mortality for salmon in their first 1-2 months at sea! yes, For every 10 fish that hatch, survive in the river and make it to the estuary we then lose 6-8 at or near the estuary. There are a lot of hypotheses for this and they are being tested this summer. For 2014 alone they are spending hundreds of thousands on research to determine what is causing this massive die-off.
Could be habitat loss (eelgrass), hardening of estuary, seal predation (yes, they eat juveniles too), bird predation, toxins, and whole host of other things. But one thing is for certain, the majority of these tagged fish are not living for long after they enter the salt water. They are not making it out past vancouver island and into the open Pacific and they are not returning as adults to be targeted for sportfishing, commerical fishing, rec fishing, etc.
The low water on the cowichan is another hurdle for any returning fish to deal with and it sucks but it doesn't change the fact that juvenile salmon survival is the biggest issue we can currently tackle. I say currently because if it turns out climate change is the big killer for juveniles and responsible for lower water levels and warmer water then we're pretty much all screwed.